Reductionism

Take a look around at everything. I mean it is safe to say that everything we see from the trees, to buildings, even to cute little dogs walking on the street are made up of smaller parts working together in a singular complex system. Biologically speaking, what is a community? A group of
interacting organisms all sharing a populated environment each fulfilling a
different niche within that environment. Well...what are organisms made of?
Organ systems, such as the cardiovascular system. Organs within that system,
such as the heart accompanied by blood vessels, which are made up of differing
epithelial tissue working with a common
goal to fulfill a specific function. What are these tissues made of?

Specialized cells which are also made up of organelles carrying out specific
functions within the cell. What are these organelles made of? Specific
macromolecules; Proteins; Lipids; Sugars. We can go even further than that and
break down one of these components. Take proteins, for example. Extremely
complex, yet made of the simple component called an amino acid, chained
together to form polypeptides. How does one make a protein? Well for one you
need to make an amino acid, which is composed of an amine group (H2N) bonded to
a central carbon which is also bonded to a carboxyl group (COOH), which is then
bonded to a hydrogen on top and also a wide range of "R" groups.
These R groups can be as simple as a single hydrogen making said amino acid a
non polar Gylcine, to a more complex chain of (CH2)4NH3+ which makes the
negatively charged Lysine. But you can't just stop here since a single amino
acid does not make a protein. Alas, we cannot neglect the 4 levels of protein
structure. We start with the primary structure, which is the unique sequence of
the various 20 amino acids, covalently bonded through peptide bonds. The
structure of the chain at this level is so meticulous that any slight change,
any deletion, or misplacement of a single amino acid has disastrous results.

Replace a glutamic acid, in hemoglobin, with Valine and you get sickle cell
anemia. But even this is just the beginning, we must move on anyway. At the
secondary level proteins fold and coil, contributing to the proteins overall
confirmation. This is due to the hydrogen bonds, which are attracted to the
more electronegative oxygen atoms which are located within the protein.
Individually these bonds are weak but because they are repeated many times over
they support the overall shape of the protein. Tertiary structure is the result
of irregular contortions due to the different types of bonding, such as
disulfide bridges, hydrophobic interactions, van der walls forces, and hydrogen
bonding. This adds a whole 'nother dynamic to protein folding which causes
proteins to twist and mold in order to conform to the shape of the bonding. At
the 4th level you have the complete aggregation of two or more polypeptide
chains into one functional macromolecule. One thing to note is that the
structure of the protein at any level accounts for its function and purpose. So
wait, function is the emergent property of structure? We can get to that later,
but for now we must go...deeper. So what even causes the sequences, amino
acids, and bonding?

For this we must look into the molecular level. I mean,
specifically, what causes hydrogen bonding? Well for starters hydrogen is an
atom containing 1 proton and one electron in the 1s orbital, so hydrogen is
pretty chill and stable yet still likes to hang around everyone. Oxygen, on the
other hand as 8 protons, 8 neutrons and 8 electrons. Its electrons fill the 2p
orbital and it is 2 electrons short of a full valence electron shell. Now what
girl...atom wants is a full valence electron shell. Some have even been
reported to cause explosions just to get full shells. This ultimately results
in oxygen's high electro negativity, which describes the tendency of an atom to
attract electrons to itself. Since oxygen just needs 2 electrons to get a full
shell it REALLLLY REALLLY wants those electrons. Fluorine would be an example
of an even more electronegative atom since it really just needs 1 so it tries
to be all buddy buddy with all the other atoms. Think of that kid who likes to
be the life of the party. On the other side of the periodic table you've got
elements like lithium and sodium which only need to lose one electron to get a
full electron shell, which means they have a low affinity for gaining
electrons. Now hydrogen bonds occur when a hydrogen atom becomes covalently
attracted to a very electronegative atom. This, in itself, describes the nature
of bonds between atoms in general. In order to fill their valence electron
shells, atoms will covalently bond, or share electrons, or sometimes completely
give and take electrons to form ionic bonds. So what's a protein? Basically a
bunch of molecules and atoms bonded together, which creates a complex system
out of a very simple one.

So through all of this we can
essentially reduce an organism to a sea of functioning parts, fulfilling different
functions due to the unique interactions of atoms, which are composed of
neutrons, protons and electrons. But...can we go further? Yeah with quarks and
all that jazz but that is completely out of my field of expertise. I honestly
think it is completely incredible that everything we see today is the result of
the emergent properties of subatomic particles. And I say emergent, as in the
movements of atoms are completely probabilistic yet they can ultimately end up
creating extremely complex systems. In fact, at the quantum level we can't
accurately predict anything with accuracy and record it at all. Heisenberg
uncertainty principal anyone? I guess we are stuck with mere probabilities of
what COULD happen, for example in the case of electron orbitals. We can't
specifically track where an electron is at any given moment but we can draw
conclusions about the probability of its placement at any given moment in time.
Yet overlay each probability upon more probabilities and you eventually get a
high order of organization. Snow? An emergent property due to the chemical properties
of water, directed by the Brownian motion of water molecules. Color? Elementary
particles neither emit nor absorb specific wavelengths of light but when you
put them together a whole array of the visible spectrum can be seen.

What causes this "emergence"? It seems that emergence is also another random
effect seen within the universe. But does this make everything a random event
or actually deterministic based on initial conditions. It can be said that due
to the nature of the expansion of the universe from a single point the physical
laws we have now were set in place, yet if any slight variables changed within
the initial conditions of the big bang the laws that we see today could be
fundamentally different. It is deterministic in that the events today are the
result of compounded events over the course of time expanding from a single point,
but it is random due to the lack of predictability of the outcomes from the
initial condition. Get what I mean? Maybe not. Well, for one thing, the only
thing I am certain of at this point is my own uncertainty.

Now let's apply emergence to the real world. For example, biology can be seen as the application or a result of the emergence of chemistry which is the application of physics which is the
application of mathematics, which is the application of ratiocination and
logic. But how far does the rabbit hole go? It seems there really can be
nothing beyond logic but logic can be derived as the application of empirical
data while also implementing ideas which are purely inductive. This is a brain
melter, but this is another debate for another day to try and ask
"What is logic?". This is about reductionism not epistemology. Let's
stick with mathematics, which is the application of logic. Well where do we
begin except with Axioms which are statements that are accepted without proof,
or basic assumptions that are self evident. For example, an axiom of equality,
x=x. This itself has to be true, I mean if something does not equal itself how
can we proceed from this? Plus it's an axiom, axioms have always gotta be true
right? They're self evident! Although it got me thinking...how do we know
central axioms ARE true. I mean could I just pull an axiom out my pocket and
say "It is self evident that all dogs are green". Is it an axiom?
Well...as a counterpoint to my hypothetical situation, it can be observed that
not all dogs are green so that axiom isn't SELF EVIDENT to be true. Saying
something is an axiom doesn't make it an axiom but from where do we even get
axioms? Sure humans are fallible, but wouldn't that mean their fallibility
could also pollute the world of axioms? Think about this dude, let's call him
Chuck Berrymore.

Now Chuck Berrymore lives in a city his whole life and all he
sees are green dogs. Just green dogs everywhere, and never in his life has he
seen anything but green dogs. Well then his axiom "All dogs are
green" is grounded in empirical data, but it is incomplete data...whatever
never mind. My question is "does the foundation of axioms go against the
idea of reductionism?". Axioms are just that, self evident, they cannot be
reduced any further. However, I guess as a counterpoint to this is that
reductionism doesn't specifically state EVERYTHING can be reduced to simpler
components. For example can x^2/x be simplified? Why yes it can, to become
merely x. It simply stays x unless some arbitrary definition is added making x
equal something else. As it stands, x=x just by applying the axiom
"Something always equals itself".

Now what if we applied this to something such as morality.
The age old question "Does objective morality exist?". I, personally
have no idea or have any knowledge regarding a standard of morality that is
universally true. It can be argued that a standard of morality lies with an all
powerful supreme being. It can also be argued that that morality is completely
subjective and differs from person to person and is also subject to change. I
mean, slavery has never been seen as an evil except within the last 200-300
years. So for much of human history it did not exactly violate any sort of
moral code. However, if morality is subjective where does it even come from in
the first place? Is it also an emergent property, derived from evolution in
order to ensure the survival of species? That could explain why murder and
incest are frowned upon. How is a moral system even created anyway? For that
you must build it around a set of axioms like "Though shalt not kill"
or "Treat others as you would like to be treated" or "Lying is
bad". I guess from there you could build off of that. I'm not clear on the
idea that morality can be seen as purely reductionist but it has its basis on
simpler ideas.

Now let's talk about human consciousness and yes I know we can't even begin to talk about
it unless we can thoroughly define what it means to be conscious. Just bear
with me here. From what I've learned so far, consciousness can be seen as the
emergent property of billions of neurons firing electrical impulses. What makes
us more conscious than a spider or a kangaroo? Our thought isn't as simple and
we don't not rely only on instinct. One defining characteristic between
organisms of lower and higher complexity seems to lie with the complexity of
the nervous system. Our abstract thought arises from the billions of
connections our neurons make, but at the base level are we simply just action
potentials responding to stimuli? Computers can be thought of in the same way.
Data is just basically billions of 1's and 0's, on and off, respectively.

However chain all those on and off switches and you can build programs which
simulate protein folding to programs that can calculate large numbers. We could
essentially be working the same way. One single neuron and a mind does not
emerge, but once you keep adding billions and allow them to form connections in
unique ways some sort of consciousness can emerge. But how exactly does a
"mind" form out of billions of neurons and at what point do you get a
human mind? If you started with a single neuron and kept adding neurons one by
one when would you obtain a human mind? Furthermore if our decisions are
determined by our brain which is merely a complex network of electrical
impulses and chemical neurotransmitters, do we really have control over our own
free will?

Let's just take one extreme example; Psychopaths. If one were to
peer into the brain of a psychopath and the brain of a normal human he/she
would see clear biological differences in the brain which would be the cause of
a Psychopath's abnormal behavior. However if the structure of their brain is
not within their control, are their actions really their fault? Now I know this
was an extreme example but let's just take a look at the decisions your brain
makes subconsciously. For example, finding some attractive is, in fact, part of
subconscious brain activity. That could explain all the stupid things you don't
intend to say when you around a person you really like. Even eating can be
considered subconscious. I mean, ever smell something really great and suddenly
you are hungry even though you weren't really hungry before? That's your brain.
Whether we like it or not our subconscious brain takes an active role in our
thought process and the decisions we make. We could even take a look at how the
brain implements what in learns in order to make future decisions. When you
were younger I'm sure curiosity got the best of you one time and you felt the
need to touch a burning hot stove or pot. It hurt right? I'm sure it did. Well
your brain archives that memory and will ultimately influence your decision in
the future on whether or not you should touch the stove. You remember the pain,
your brain remembers the pain, but is it YOUR decision? Of course I'm
neglecting our ability to override our natural fail safes and I am completely
oversimplifying whether or not our experiences even impact our freewill and I
haven't even defined free will anyway. Rambling at this point, but I'm tired
and it is "whatever".

Even through
all of this we should not forget that even though everything, including
ourselves can be reduced to simple parts, it is really the complete whole that
tends to matter. Yeah everything is atoms and what not but that doesn't make a
tree any less beautiful than it already is. Reductionism at its core breaks
down complex systems into their components. However, I think there's a limit to
how far something can be broken down. At the very core there has to be
something right? This all raises the ultimate question for me. How far down
does the universe, matter, and energy go? I mean hell, what specifically CAUSED
the big bang and eventually made everything we see today, from atoms to
molecules to cells to organisms. Is the universe itself an emergent property?

Jesus Christ I hate this formatting.

Emergence:
http://www.youtube.com/watch?v=5E9DoN_5BjY

Reductionsim In biology:
http://plato.stanford.edu/entries/reduction-biology/

Complex Theory of Consciousness:
http://www.scientificamerican.com/article.cfm?id=a-theory-of-consciousness